MolNFT v1 · #91426 · protein

S.POMBE MRE11 apoenzym

4FCX · DNA repair protein RAD32: “S.POMBE MRE11 apoenzym”. X-ray diffraction, 1 ligand (MN), 6 pockets (best druggability 0.64). MolNFT v1 #91426 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4FCX
Type: protein
Length: 735 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA repair protein RAD32
UniProt: Q09683
Ligands: MN
Pockets: 6 · best druggability 0.64

Structure

x-ray diffraction · 2 distinct chains · 24% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	DNA repair protein RAD32	protein	369	23% helix, 26% strand	Q09683
A	DNA repair protein RAD32	protein	366	26% helix, 27% strand	Q09683

Ligands and binding sites

MN · Manganese (II) ion · metal · 4 copies · chains B, A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	72	0.64	0.92	27	empty
2	84	0.47	0.81	16	empty
3	176	0.46	0.75	30	empty
4	119	0.43	0.77	21	empty
5	73	0.41	0.80	24	empty

Interfaces

1 interface between chains.

B–A · 2126 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

4FCX · S.pombe Mre11 apoenzym · the same entry in another collection · chain B against B, TM-score 1.00
Q09683 · AlphaFold monomer V2.0 prediction for DNA repair protein RAD32 (Q09683) · a predicted model of the same protein · chain A against A, TM-score 0.95

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q09683
Elsewhere: RCSB PDB 4FCX · PDBe 4FCX · UniProt Q09683

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